EBI Databases InterPro	Search Open in usermanual InterPro:
Jump to: InterProScan Databases Documentation FTP site Help Click on the icon for context sensitive help from the user manual. Advanced search

InterPro: IPR012287 Homeodomain-related

Protein matches Help

UniProtKB

Matches:

62373 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR012287 Homeodomain-rel

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Gene3D	G3DSA:1.10.10.60	Homeodomain-rel	62373
Signatures in BioMart

InterPro Relationships Help

Parent

IPR009057 Homeodomain-like

Children

IPR000005 Helix-turn-helix, AraC type
IPR001005 SANT, DNA-binding
IPR001356 Homeobox
IPR001647 Transcriptional regulator, TetR-like, DNA-binding, bacterial/archaeal
IPR015010 Rap1 Myb

Found in

IPR000268 RNA polymerases, N/8kDa subunit
IPR003022 Transcription factor Otx2
IPR003025 Transcription factor Otx
IPR006695 Centromere protein Cenp-B, DNA-binding domain 1
IPR012738 Transcriptional regulator, DhaS
IPR015126 Mu DNA binding, I gamma subdomain
IPR017053 Response regulator, plant B-type
IPR017930 HTH transcriptional regulator, Myb-type, DNA-binding
IPR018060 Helix-turn-helix, AraC domain
IPR019915 Transcriptional regulator, pyrimidine utilisation, RutR

Contains

IPR000047 Helix-turn-helix motif, lambda-like repressor
IPR001827 Homeobox protein, antennapedia type, conserved site
IPR002197 Helix-turn-helix, Fis-type
IPR004906 Pogo transposase / Cenp-B / PDC2, subgroup, DNA-binding HTH domain
IPR014778 Myb, DNA-binding
IPR017970 Homeobox, conserved site
IPR020479 Homeobox, region
IPR020789 RNA polymerases, subunit N, zinc binding site

GO Term annotation Help

Process

GO:0045449 regulation of transcription

Function

GO:0003677 DNA binding

InterPro annotation

Entry Details in BioMart

Abstract

Homeodomain proteins are transcription factors that share a related DNA binding homeodomain [1]. The homeodomain was first identified in a number of Drosophila homeotic and segmentation proteins, but is now known to be well conserved in many other animals, including vertebrates. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure. Many proteins contain homeodomains, including Drosophila Engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and HOX proteins.

The homeodomain motif is very similar in sequence and structure to domains in a wide range of DNA-binding proteins, including recombinases, Myb proteins, GARP response regulators, human telomeric proteins (hTRF1), paired domain proteins (PAX), yeast RAP1, centromere-binding proteins CENP-B and ABP-1, transcriptional regulators (TyrR), AraC-type transcriptional activators, and tetracycline repressor-like proteins (TetR, QacR, YcdC) [2, 3, 4].

Structural links Help

PDB - click here

SCOP: a.35.1.7 , a.4.1.1 , a.4.1.11 , a.4.1.12 , a.4.1.2 , a.4.1.3 , a.4.1.4 , a.4.1.6 , a.4.1.7 , a.4.1.8 , a.4.1.9 , a.4.11.1 , a.6.1.7 , b.82.4.1 , i.11.1.1 , i.8.1.1 , j.92.1.1

CATH: 1.10.10.10 , 1.10.10.60 , 1.10.260.40 , 1.10.357.10

Interactions Help

This domain has been experimentally proven to be involved in Protein:Protein interactions.
Representative data is shown with the following example proteins:

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR012287

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O08755 Hepatocyte nuclear factor 6

O14529 Homeobox protein cut-like 2

P01366 Mating-type protein A1

P02833 Homeotic protein antennapedia

P34257 Transposable element Tc3 transposase

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR020479	Homeobox, region
IPR017995	Homeobox protein, antennapedia type
IPR001827	Homeobox protein, antennapedia type, conserved site
IPR012287	Homeodomain-related
IPR017970	Homeobox, conserved site
IPR003350	Homeodomain protein CUT
IPR001356	Homeobox
IPR009057	Homeodomain-like
	PDB Chain
	ModBase
	CATH Domain
	SWISS-MODEL
	SCOP Domain

Publications Open in usermanual
1.	Mannervik M. Target genes of homeodomain proteins. Bioessays 21 267-70 1999 [PubMed: 10377888] http://dx.doi.org/10.1002/(SICI)1521-1878(199904)21:4<267::AID-BIES1>3.3.CO;2-3
2.	Hosoda K, Imamura A, Katoh E, Hatta T, Tachiki M, Yamada H, Mizuno T, Yamazaki T. Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. Plant Cell 14 2015-29 2002 [PubMed: 12215502] http://dx.doi.org/10.1105/tpc.002733
3.	Nishikawa T, Nagadoi A, Yoshimura S, Aimoto S, Nishimura Y. Solution structure of the DNA-binding domain of human telomeric protein, hTRF1. Structure 6 1057-65 1998 [PubMed: 9739097] http://dx.doi.org/10.1016/S0969-2126(98)00106-3
4.	Kisker C, Hinrichs W, Tovar K, Hillen W, Saenger W. The complex formed between Tet repressor and tetracycline-Mg2+ reveals mechanism of antibiotic resistance. J. Mol. Biol. 247 260-80 1995 [PubMed: 7707374] http://dx.doi.org/10.1006/jmbi.1994.0138

Additional Reading Open in usermanual
	Religa TL. Comparison of multiple crystal structures with NMR data for engrailed homeodomain. J. Biomol. NMR 40 2008 189-202 [PubMed: 18274703] http://dx.doi.org/10.1007/s10858-008-9223-9
	Resch M, Striegl H, Henssler EM, Sevvana M, Egerer-Sieber C, Schiltz E, Hillen W, Muller YA. A protein functional leap: how a single mutation reverses the function of the transcription regulator TetR. Nucleic Acids Res. 36 2008 4390-401 [PubMed: 18587152] http://dx.doi.org/10.1093/nar/gkn400
	Aleksandrov A, Schuldt L, Hinrichs W, Simonson T. Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study. J. Mol. Biol. 378 2008 898-912 [PubMed: 18395746] http://dx.doi.org/10.1016/j.jmb.2008.03.022
	Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131 2007 530-43 [PubMed: 17981120] http://dx.doi.org/10.1016/j.cell.2007.09.024
	Hirata A, Klein BJ, Murakami KS. The X-ray crystal structure of RNA polymerase from Archaea. Nature 451 2008 851-4 [PubMed: 18235446] http://dx.doi.org/10.1038/nature06530
	Ko S, Jun SH, Bae H, Byun JS, Han W, Park H, Yang SW, Park SY, Jeon YH, Cheong C, Kim WT, Lee W, Cho HS. Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins. Nucleic Acids Res. 36 2008 2739-55 [PubMed: 18367475] http://dx.doi.org/10.1093/nar/gkn030

InterPro 24.0